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Table 1 Ordered (1) and disordered (2) reaction mechanisms for multistate phosphorylation

From: Multistate Model Builder (MSMB): a flexible editor for compact biochemical models

Reaction

Type

Rate law

1. XP(i {0:N-1 }) + Kin -> XP(succ(i)) + Kin

MA

k

2. XP(i {0:N-1 }) + Kin -> XP(succ(i)) + Kin

UD

dis(N,XP.i,k,XP,Kin)

Function definition

Equation

dis(GLQ N, SITE i, GLQ k, SUB X, SUB K)

(N-i) * k * X * K

  1. Case 2 depends on the number of unphosphorylated states, so its rate law has to be expressed using a user defined (UD) type (instead of using mass action, MA) with a rate law function, called “dis”. The function definition is also shown. Each formal parameter has a different type (GLQ for global quantity, SITE to refer to the numerical state value of a site of a multistate species, and SUB for the substrate of the current reaction).
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BMC Systems Biology

ISSN: 1752-0509

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